In Orientals, genetic deficiency of ALDH2 is associated with the flushing reaction, an adverse response to alcohol. The allele ALDH-2-2 with the transition G/C-greater than A/T 12 bp from the 3'-end of exon 12 is responsible for the deficiency. Our primer-allele-specific amplification assay (PASA) of exon 12 did not reveal the existence of the same allele in South American Indians in whom the enzyme deficiency has been reported. This negative finding prompted further search for the possible mutations across the entire coding sequence of the ALDH-2 gene within a sample of 35 South American Indians from seven tribes. A RT-PCR assay detected low levels of ALDH-2 expression in human lymphoblasts. This allowed us to develop a RT-PCR-SSCP assay to detect mutations in the coding sequence. The coding sequence of ALDH-2 cDNA was PCR amplified as partially overlapped fragments. Each fragment was digested with restriction endonuclease, and subfragments of 148-285 bp in length were subjected to single-stranded conformation polymorphism (SSCP) analysis. Thus far, two rare SSCP variants have been detected in the proximal (3'-end) part of ALDH-2 gene that corresponds to exons 11-13. These variants are being sequenced and the search for mutations is being continued in the middle part of the coding sequence and in the 5'flanking (promoter) region.